6-29942594-C-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_002116.8(HLA-A):c.41C>G(p.Ser14Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S14L) has been classified as Uncertain significance.
Frequency
Consequence
NM_002116.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HLA-A | NM_002116.8 | c.41C>G | p.Ser14Trp | missense_variant | 1/8 | ENST00000376809.10 | |
LOC124901298 | XR_007059541.1 | n.813+2187G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HLA-A | ENST00000376809.10 | c.41C>G | p.Ser14Trp | missense_variant | 1/8 | NM_002116.8 | P3 | ||
ENST00000429656.1 | n.474G>C | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 104268Hom.: 0 Cov.: 17 FAILED QC
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1002368Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 499660
GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 104268Hom.: 0 Cov.: 17 AF XY: 0.00 AC XY: 0AN XY: 50196
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at